I noticed something funny happening in my last week's set or orders after a sale was made in ebay and pulled into my woocommerce orders. All of a sudden the shipping amount is not being posted into the order details. I realized it when printing out the invoice via the woocommerce print invoice plugin. I'm not sure if it's a problem with woocommerce, wp-lister, ebay, or paypal.

I take it that you're using WP-Lister Pro as the free version doesn't create orders in WooCommerce, and I'd recommend that you update to the latest beta versions, which currently is 1.3.4.7 and which should fix this issue.